Unequal branch lengths

PIP
Here is the abstract, with some brief comments by me [inline in braces]

Abstract:

I attempt to sketch a unified picture of the origin of living

organisms in their genetic, bioenergetic, and structural aspects.

Only selection at a higher level than for individual selfish

genes could power the cooperative macromolecular coevolution

required for evolving the genetic code. The protein synthesis

machinery is too complex to have evolved before membranes. [Hooray!]

Therefore a symbiosis of membranes, replicators, and catalysts

probably mediated the origin of the code and the transition

from a nucleic acid world of independent molecular replicators

to a nucleic acid/protein/lipid world of reproducing organisms.

[I see it as a transition from a world of lipid-based reproducing

organisms without nucleic acids to one with them. But I can live

with the way he expressed it.] Membranes initially functioned

as supramolecular structures to which different replicators

attached and were selected as a higher-level reproductive unit:

the proto-organism. [Hooray!] I discuss the roles of stereochemistry,

gene divergence, codon capture, and selection in the code's origin.

I argue that proteins were primarily structural not enzymatic [Ok]

and that the first biological membranes consisted of amphipathic

peptidyl-tRNAs and prebiotic mixed lipids. [Boo! There were no

prebiotic mixed lipids. But the idea that peptidyl tRNAs were

an important membrane component just after the start of translation

is quite similar to my ideas.]

The peptidyl-tRNAs functioned as genetically-specified lipid

analogues with hydrophobic tails (ancestral signal peptides)

and hydrophilic polynucleotide heads. Protoribosomes arose

from two cooperating RNAs: peptidyl transferase (large subunit)

and mRNA-binder (small subunit). Early proteins had a second

key role: coupling energy flow to the phosphorylation of gene

and peptide precursors, [Hooray!] probably by lithophosphorylation

by membrane-anchored kinases scavenging geothermal polyphosphate

stocks. [Boo! I prefer PMF and perhaps even photophosphorylation.]

These key evolutionary steps probably occurred on the outer surface

of an 'inside out-cell' or obcell, [Yeah, I already knew that.]

which evolved an unambiguous hydrophobic code with four prebiotic

[Boo!] amino acids and proline, and initiation by isoleucine

anticodon CAU; early proteins and nucleozymes were all

membrane-attached. [Hooray!] To improve replication, translation,

and lithophosphorylation, hydrophilic substrate-binding and catalytic

domains were later added to signal peptides, yielding a ten-acid

doublet code. [Doublet?] A primitive proto-ecology of molecular

scavenging, parasitism, and predation evolved among obcells. I

propose a new theory for the origin of the first cell: fusion of

two cup-shaped obcells, or hemicells, to make a protocell with

double envelope, internal genome and ribosomes, protocytosol, and

periplasm. [You are getting fancy now, Tom. You used to have only

one cup folding on itself.] Only then did water-soluble enzymes

[Hooray!], amino acid biosynthesis [Boo!], and intermediary

metabolism [Mixed response] evolve in a concentrated autocatalytic

internal cytosolic soup, causing 12 new amino acid assignments,

termination, and rapid freezing of the 22-acid code. Anticodons

were recruited sequentially: GNN, CNN, INN, and *UNN. CO2 fixation,

photoreduction, and lipid synthesis probably evolved in the

protocell before photophosphorylation. [I think they evolved before

any kind of phosphorylation - before nucleic acids] Signal

recognition particles, chaperones, compartmented proteases,

and peptidoglycan arose prior to the last common ancestor of

life, a complex autotrophic, anaerobic green bacterium. [Yep.]

Tom
Well you certainly won't find an Occam's razor in the jumble above.
I see the same problems here that I see with all origin scenarios -
no mention of the environment, and no mention of any reason why any of this
would
happen, or any power/force that would start it, or continue it, or force
it to adapt to it. Talk about a prebiotic soup - this is a real murky
gumbo!

If we learn anything from Mother nature, or her patterns, it is that
her methods are never erudite. They are simple, basic, and reasonable.
She hates unconnected complexity. She hates chance, and uses it
very seldomly. And the more we learn the less fluke factor we find!

I'm afraid all I see here is another origin scenario in the same pattern
that I call "5 steps of a magic chemical wand' (though there are many
more than 5 steps here)

If not the sun -
a magic wand
it's the only other choice
for the o-ri-gin.

.

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